This pipeline assembles genomes starting from long-read Oxford Nanopore sequences. It uses the data flow language nextflow to coordinate the steps in the pipeline, which involves:
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Read-level quality control
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Basecalling with Guppy
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Read adapter trimming
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De novo or reference-guided assembly with different assemblers and parameters
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Automated assessment of the assembly
nextflow pull luslab/oist-assembler
To run this pipeline, you will need Nextflow and Docker (or Singularity). If you are planning to use GPU-accelerated basecalling, you'll also need a CUDA-capable GPU and the NVIDIA Container Toolkit.
In this repository clone:
nextflow run main.nf -profile <oist,crick> --input test_workflows/assembly_1.metadata.csv
Directly from GitHub:
nextflow run luslab/oist-assembler -profile <oist,crick> --input [metadata.csv]
In this repository clone:
nextflow run main.nf -config [pipeline.config] --input [metadata.csv]
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